pepfrag package

Module contents

class pepfrag.Mass(mono: float, avg: float)

Bases: object

Represents a mass pair of monoisotopic and average masses.

Parameters:

• mono – Monoisotopic mass.
• avg – Average mass.

class pepfrag.MassType

Bases: enum.Enum

An enumeration representing the possible mass types.

Note that the values of these enumerations correspond to their index in Mass, and similarly in the C++ code underneath methods such as calculate_mass.

mono = 0

Monoisotopic mass

avg = 1

Average mass

class pepfrag.IonType

Bases: enum.Enum

Enumeration of possible fragment ion types.

precursor = 1

Precursor ions

imm = 2

Immonium ions

b = 3

b-type ions

y = 4

y-type ions

a = 5

a-type ions

c = 6

c-type ions

z = 7

z-type ions

x = 8

x-type ions

class pepfrag.ModSite(mass: float, site: Union[int, str], mod: str)

Bases: object

Class representing an instance of mod_name at position site.

Parameters:

• mass – Mass of the modification.
• site – Position of the modification. Integer for sequence position, ‘nterm’ for N-terminus or ‘cterm’ for C-terminus.
• mod – Name of the modification.

class pepfrag.Peptide(sequence: str, charge: int, modifications: Sequence[pepfrag.pepfrag.ModSite], mass_type: pepfrag.constants.MassType = <MassType.mono: 0>, radical: bool = False)

Bases: object

A class to represent a peptide, including its charge state and any modifications, including PTMs and quantitative tags. The class should be used to fragment the peptides for mass spectrum annotation.

mass_type

Type of masses used in calculations (see MassType).

radical

Flag indicating whether the peptide is a radical peptide.

peptide_mass

The mass of the peptide along the sequence, with each position calculated separately.

Note

In the returned list, index 0 is the N-terminus mass, while index -1 is the C-terminus mass.

mass

Total mass of the peptide, including modifications.

mz

Calculates the mass-to-charge ratio of the peptide.

calculate_mass() → List[float]

Calculates the theoretical mass of the peptide along the sequence, including any modifications.

Returns:Masses along the peptide sequence. Index 0 is the N-terminus mass, while index -1 is the C-terminus mass.

fragment(ion_types: Optional[Dict[pepfrag.pepfrag.IonType, List[Union[str, Tuple[str, float]]]]] = None) → List[Tuple[float, str, int]]

Fragments the peptide to generate the ion types specified.

Parameters:ion_types – Dictionary of IonType s to list of configured neutral losses. Only fragments for IonType s specified here will be generated. Returns:List of generated ions, as tuples of (fragment mass, ion label, sequence position).